NAME

Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace

SYNOPSIS

    # get a Bio::Seq::Qual compliant object somehow
          $st = &get_object_somehow();

    # to test this is a seq object
          $st->isa("Bio::Seq::TraceI") 
               || $obj->throw("$obj does not implement the Bio::Seq::TraceI interface");

          # set the trace for T to be @trace_points
     my $arrayref = $st->trace("T",\@trace_points);
          # get the trace points for "C"
     my $arrayref = $st->trace("C");
          # get a subtrace for "G" from 10 to 100 
     $arrayref = $st->subtrace("G",10,100);
          # what is the trace value for "A" at position 355?
     my $trace_calue = $st->traceat("A",355);
          # create a false trace for "A" with $accuracy
     $arrayref = $st->false_trace("A",Bio::Seq::Quality, $accuracy);
          # does this trace have entries for each base?
     $bool = $st->is_complete();
          # how many entries are there in this trace?
     $length = $st->length();

DESCRIPTION

This object defines an abstract interface to basic trace information. This information may have come from an ABI- or scf- formatted file or may have been made up.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chad Matsalla

Email bioinformatics@dieselwurks.com

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Implementation Specific Functions

These functions are the ones that a specific implementation must define.

trace($base,\@new_values)

 Title   : trace($base,\@new_values)
 Usage   : @trace_Values  = @{$obj->trace($base,\@new_values)};
 Function: Returns the trace values as a reference to an array containing the
     trace values. The individual elements of the trace array are not validated
     and can be any numeric value.
 Returns : A reference to an array.
 Status  : 
Arguments: $base : which color channel would you like the trace values for?
               - $base must be one of "A","T","G","C"
          \@new_values : a reference to an array of values containing trace
               data for this base

subtrace($base,$start,$end)

 Title   : subtrace($base,$start,$end)
 Usage   : @subset_of_traces = @{$obj->subtrace("A",10,40)};
 Function: returns the trace values from $start to $end, where the
        first value is 1 and the number is inclusive, ie 1-2 are the first
        two trace values of this base. Start cannot be larger than end but can
        be equal.
 Returns : A reference to an array.
 Args    : $base: "A","T","G" or "C"
          $start: a start position
          $end  : an end position

can_call_new()

 Title   : can_call_new()
 Usage   : if( $obj->can_call_new ) {
             $newobj = $obj->new( %param );
         }
 Function: can_call_new returns 1 or 0 depending on whether an
        implementation allows new constructor to be called. If a new
        constructor is allowed, then it should take the followed hashed
        constructor list.
           $myobject->new( -qual => $quality_as_string,
                           -display_id  => $id,
                           -accession_number => $accession,
                           );
 Example :
 Returns : 1 or 0
 Args    :

traceat($channel,$position)

 Title   : qualat($channel,$position)
 Usage   : $trace = $obj->traceat(500);
 Function: Return the trace value at the given location, where the
        first value is 1 and the number is inclusive, ie 1-2 are the first
        two bases of the sequence. Start cannot be larger than end but can
        be equal.
 Returns : A scalar.
 Args    : A base and a position.

length()

 Title   : length()
 Usage   : $length = $obj->length("A");
 Function: Return the length of the array holding the trace values for the "A"
     channel. A check should be done to make sure that this Trace object
     is_complete() before doing this to prevent hazardous results.
 Returns : A scalar (the number of elements in the quality array).
 Args    : If used, get the traces from that channel. Default to "A"

trace_indices($new_indices)

 Title   : trace_indices($new_indices)
 Usage   : $indices = $obj->trace_indices($new_indices);
 Function: Return the trace iindex points for this object.
 Returns : A scalar
 Args    : If used, the trace indices will be set to the provided value.